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comparison make.shared.xml @ 1:5f23107faaa8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 04:28:22 -0400
parents e9d1265e868e
children 35e4be39c33d
comparison
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0:e9d1265e868e 1:5f23107faaa8
1 <tool profile="16.07" id="mothur_make_shared" name="Make.shared" version="@WRAPPER_VERSION@.0" force_history_refresh="True"> 1 <tool profile="16.07" id="mothur_make_shared" name="Make.shared" version="@WRAPPER_VERSION@.0">
2 <description>Make a shared file from a list and a group</description> 2 <description>Make a shared file from a list and a group</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$intype.otu" intype_otu.dat && 13 ln -s "$intype.otu" intype_otu.dat &&
11 #if $intype.infile == "otulist": 14 #if $intype.infile == "otulist":
12 ln -s "$intype.group" intype_group.dat && 15 ln -s "$intype.group" intype_group.dat &&
13 #end if 16 #end if
29 #end if 32 #end if
30 list=intype_otu.dat 33 list=intype_otu.dat
31 #end if 34 #end if
32 )' 35 )'
33 | sed 's/ //g' ## mothur trips over whitespace 36 | sed 's/ //g' ## mothur trips over whitespace
34 | mothur && 37 | mothur
38 | tee mothur.out.log &&
35 39
36 ## move output files to correct destination 40 ## move output files to correct destination
37 mv mothur.*.logfile "$logfile" && 41 mv mothur.*.logfile "$logfile" &&
38 #if $intype.infile == 'otulist' and $intype.groups: 42 #if $intype.infile == 'otulist' and $intype.groups:
39 mv intype_otu*.groups "$groupout" 43 mv intype_otu*.groups "$groupout"
66 </inputs> 70 </inputs>
67 <outputs> 71 <outputs>
68 <expand macro="logfile-output"/> 72 <expand macro="logfile-output"/>
69 <data name="shared" format="mothur.shared" from_work_dir="intype_otu*.shared" label="${tool.name} on ${on_string}: shared"/> 73 <data name="shared" format="mothur.shared" from_work_dir="intype_otu*.shared" label="${tool.name} on ${on_string}: shared"/>
70 <data name="groupout" format="mothur.groups" from_work_dir="intype_otu*.groups" label="${tool.name} on ${on_string}: groups"> 74 <data name="groupout" format="mothur.groups" from_work_dir="intype_otu*.groups" label="${tool.name} on ${on_string}: groups">
71 <filter>groups</filter> 75 <filter>intype['group'].ext == "mothur.groups"</filter>
72 </data> 76 </data>
73 <collection name="labelshares" type="list" label="${tool.name} on ${on_string}: share files per label"> 77 <collection name="labelshares" type="list" label="${tool.name} on ${on_string}: share files per label">
74 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared" format="mothur.shared"/> 78 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared" format="mothur.shared"/>
75 <filter>groups</filter> 79 <filter>intype['groups']</filter>
76 </collection> 80 </collection>
77 </outputs> 81 </outputs>
78 <tests> 82 <tests>
79 <test><!-- test with biom file --> 83 <test><!-- test with biom file -->
80 <param name="infile" value="biom"/> 84 <param name="infile" value="biom"/>
105 <help> 109 <help>
106 <![CDATA[ 110 <![CDATA[
107 111
108 @MOTHUR_OVERVIEW@ 112 @MOTHUR_OVERVIEW@
109 113
110 **Command Documenation** 114 **Command Documentation**
111 115
112 The make.shared_ command takes a list_ and a group_ file and outputs a shared_ file, as well as a rabund_ file for each group. 116 The make.shared_ command takes a list_ and a group_ file and outputs a shared_ file, as well as a rabund_ file for each group.
113 117
114 118
115 .. _list: http://www.mothur.org/wiki/List_file 119 .. _list: https://www.mothur.org/wiki/List_file
116 .. _group: http://www.mothur.org/wiki/Group_file 120 .. _group: https://www.mothur.org/wiki/Group_file
117 .. _shared: http://www.mothur.org/wiki/Shared_file 121 .. _shared: https://www.mothur.org/wiki/Shared_file
118 .. _rabund: http://www.mothur.org/wiki/Rabund_file 122 .. _rabund: https://www.mothur.org/wiki/Rabund_file
119 .. _make.shared: http://www.mothur.org/wiki/Make.shared 123 .. _make.shared: https://www.mothur.org/wiki/Make.shared
120 ]]> 124 ]]>
121 </help> 125 </help>
122 <expand macro="citations"/> 126 <expand macro="citations"/>
123 </tool> 127 </tool>